The Great Pokemon Conspiracies: Missingno
by Cheese Nachos Supreme
Summary: Two otherwise unrelated Pokemon. A murder. The missing link.
1. Murky Waters

**The Great Pokemon Conspiracies:**

**~Missingno.~**

**...**

**PROLOGUE**

The Pokémon world is a world of adventures and dreams. In them, the hero, you, always sets out on an adventure with a trusted Pokémon partner to defeat the Gym Leaders, the Pokémon League, and finally, the Champion. The hero always has a rival who barges in at totally the wrong times and challenges him or her to battle. There is always a criminal gang trying to do something intolerable, but luckily, the hero always interferes and foils their plans. And, along the journey, the hero always learns new lessons and becomes a better person.

That is the Pokémon world everyone knows. Now this story will introduce you to a different side of it. You will see the Pokémon world with new eyes, and what you will see is darker.

Much darker.

...

* * *

**Chapter One: Murky Waters**

⌣»̶✽«̶ There's this little town on the east of Kanto. It's called Lavender Town, and it claims as the 'town with the purple hue'. Gravelerette complains why it had chosen purple as its color instead of pink. I explained to her that well, Lavender Town wants to be known as a noble town, and purple IS a noble color. Besides, there isn't anything she can do about it, is there?

Lavender Town is small and rather has a sad, dismal air to it. It also has very few people living in it.

The houses there are small and rather insignificant. The only things that stand out are their purple roofs. I guess Lavender Town people ARE really keen on promoting their town as a noble town with a purple hue.

The most significant thing in the town, however, is the tower on the north-east of it. It's old and crumbling, and from the sign near its front door, we can tell that it was a Pokémon cemetery.

LOST TOWER

MAY POKÉMON SPIRITS REST EASY

Gravelerette complained non-stop that she would never go into it, but again, she had no choice for it was the only building in Lavender Town our Trainer Kammy hasn't explored yet. Besides, what could happen to us in a Pokémon cemetery, anyway?

Well, after this particular adventure, I take back my words, for the strangest, weirdest, most supernatural thing happened, which almost got me, sensible Venusaur, scared out of my wits.

Almost.

...

"Hello. Are you a Trainer?" the woman standing next to Kammy in the Pokémon Center line asked.

"Oh, yes, ma'am," Kammy said politely as she handed over the Poké Balls containing her Pokémon to the nurse at the desk to be restored to full health.

"If you're a Trainer, then you must know about Team Rocket," the woman said. Kammy turned to her, for she suddenly sounded flustered.

"Yes, ma'am," replied Kammy. "I have heard of Team Rocket. In Saffron City, they tried to take over Silph Co." She didn't mention that it was her who finally drove Team Rocket out of Saffron City.

In case you didn't know, Team Rocket is this notorious gang of people who likes to steal other people's Pokémon. Kammy has been hot on their trail as well as challenging the Gym Leaders.

"Oh, they've bailed out of Saffron City, maybe," the woman scowled. "But now they've entered Lavender Town instead!"

"Really? What did they do? Did they steal more Pokémon?"

"Oh, worse than that," the woman grumbled. "You see, there's this cute little Cubone - we often see him scampering around Lavender Town."

Kammy nodded.

"... And Cubone's mother was one of the Pokémon the Rockets captured," the woman went on.

"And then?"

"And then, of course Cubone's mother tried to get away from those dreadful people," she said. "But guess what! As she was trying to get away, she was killed! By the Rockets!"

...

See what I mean? Things aren't going to get more normal from now on. In fact, the more you put your head under these waters, the murkier it gets.


	2. The Volunteer House

**The Great Pokemon Conspiracies:**

**~Missingno.~**

**...**

**Chapter Two: The Volunteer House**

"Oh! That's horrible!" Kammy gasped. She knew the Rockets were awful, but she never would have guessed they would go to such lengths.

"I know, isn't it," the woman grumbled. "That's left poor Cubone motherless."

"I'm sorry," Kammy sighed. "Where is Cubone now?"

"Oh, he's staying at the Pokémon Volunteer House," the woman said. "I've already visited the little guy. He's still very sad and lonely. Cries a lot."

Kammy knew what the Volunteer House was - it was a shelter for homeless Pokémon and those who have been abandoned by their Trainers.

"Oh, OK. Thank you for telling me this," Kammy said politely. "I think after this, I'll go and visit Cubone."

Since Lavender Town was so small, it didn't even take us five minutes to walk over to the Pokémon Volunteer House.

"Yay! I'm going to see Pidgey again!" exclaimed Diglett, referring to his friend who he usually played tag with.

We entered the house and saw the usual two kids playing with the Pokémon there, a boy and a girl. We also saw Diglett's Pidgey, a female Nidoran and a male one, and a Rattata.

But there was one Pokémon we haven't seen before: a small light brown Pokémon with a white head sitting in the corner, keeping his back to us.

The girl followed Kammy's gaze. "Oh, that's our newest Pokémon. His name is Cubone. We took him in when he lost his mother. Poor little fellow."

"Yes, I heard that she was killed when trying to get away from the Rockets," Kammy said. "Can we stroke him?"

"Oh, yeah, you can," the boy spoke up. "But Cubone's still a bit shy and lonely. He doesn't have many friends yet here in the Volunteer House."

Kammy went over, saying gently, "Hi, Cubone. Don't be afraid. We're not going to hurt you."

When Kammy was a few steps away from the lonely Cubone, he suddenly turned to look at her.

Gravelerette gasped, for it wasn't Cubone's head that was white. Cubone was wearing a Pokémon skull over his head! The skull had two holes where its eyes had been, but now had been converted into convenient peepholes for Cubone to see through. Cubone was also holding a bone club.

"Umm, hello," Kammy said uncertainly. She still went over and stroked his head, which was a bit weird since Cubone's head was made of bone. "There, there, Cubone."

Cubone did nothing but cry. His cries made the skull on his head rattle. "Oh, don't worry, it's not your fault," the girl said quickly when Kammy looked guilty. "He's been crying since he came here."

"Oh, poor thing," murmured Gravelerette.

After a while, Kammy decided that it was time to go.

"Where are we going next?" Diglett asked. "I was thinking of visiting the Lost Tower," Kammy replied.

"The Lost Tower?" the boy spoke up. "That's where Cubone's mother was buried."

"What- wait!" Gravelerette gasped. "You mean we're going INTO the cemetery?!" She turned to Kammy.

"Yes, and we'll visit Cubone's mother, too," Kammy decided. "Besides, it's a good place to train."

So, we went on our way, with Gravelerette stammering "Wait! But- but- but-" along the way.

Meanwhile, the kids at the Volunteer House had no idea that a pair of ears had pricked up on hearing the name the Lost Tower, and no idea at all that someone had slipped out of the door after Kammy, his bone club dragging on the floor.


	3. Lost Souls

**The Great Pokemon Conspiracies:**

**~Missingno.~**

**...**

**Chapter Three: Lost Souls**

"No," said Gravelerette. "No, I am definitely not going in there."

Gravelerette is Kammy's most docile Pokémon. She is a very feminine Graveler who's almost always forcing us to call her Gravelerette instead of Graveler.

The other Pokémon in Kammy's party are Diglett, who's young but full of sunshine; Ekans, who is not that young but isn't full of sunshine; and Machop, the exact opposite of Gravelerette - she's a total tomboy and loves battles.

"Oh come on," Ekans snarled. "It'll be interesting." "It will not be interesting!" Gravelerette cried.

"Please, Gravelerette," sighed Kammy. "We need more training, and this is the only place we haven't explored yet."

"Come on, Gravelerette," I said.

"Yeah, come on!" cried Diglett.

"Come on," hissed Ekans.

"Don't be such a baby," scolded Machop.

"FINE!" Gravelerette finally cried. "I'll go in with you. But believe me, I bet it is NOT going to be interesting."

"Whew!" Kammy sighed in relief. "Finally. OK, everyone, follow me!" And we entered the Lost Tower.

On the first floor, there were a few people milling about. Some were mourning over their departed Pokémon, and some were just about to come outside.

"This doesn't look like a cemetery," Machop said flatly. The first floor of the Lost Tower was rather empty except for a sleepy-eyed woman sitting behind a counter.

"I didn't know cemeteries also have receptionists," Diglett pointed out. "I think the real cemetery is on the second floor," Kammy told them. "Let's go!"

"Let's not," Gravelerette wailed, but no one paid her any attention. We went up the stairs onto the second floor.

Kammy was right - the real cemetery was on the second floor. There were rows and rows of tombstones bearing Pokémon names. Some had flowers scattered above them. There were a few people in the area, staring down at some tombstones.

"I think they're mediums," Ekans hissed excitedly.

Kammy was about to walk ahead to look for Cubone's mother's tomb, but she hadn't even taken a few steps when a medium stopped her.

"You are trainer?" she rasped. Kammy answered that she was.

The medium looked at her strangely. Then she began to chant some strange words.

"I see something," she murmured. "Something forbidding is in the tower. I can sense it."

"Huh?" Kammy looked confused, but Ekans was interested and entranced.

"There is a being in this tower, on the floor below the very top," the medium went on. "A being that isn't supposed to be here. A lost soul..."


	4. Close Encounters of the Undead Kind

**The Great Pokemon Conspiracies:**

**~Missingno.~**

**...**

**Chapter Four: Close Encounters of the Undead Kind**

"What!" Gravelerette burst out. "You mean a ghost?!"

The medium blinked, suddenly losing the weird look she'd got in her eyes. "Well, yes, you can say that," she said. "Although I prefer to call it a 'lost soul' or a 'wandering spirit'."

"Right. No difference," Machop mumbled, but Kammy's mouth was in a perfect O.

"I think it's best to send it on its way," said the medium. "You mean into the afterlife?" Diglett asked, and she nodded. She turned to Kammy again. "You are Pokémon trainer, no?"

"Yes," said Kammy for the second time.

"Maybe you can do something about it," the medium said. "The wandering spirit, I mean."

"Why us?" Gravelerette cowered. "Why don't you? You're a medium, right? You can talk to spirits, right? You can tell it to go away."

"Oh, no, I'm afraid we can't," the medium said. "We don't usually communicate with neither wandering spirits nor lost souls. They're bad omen."

Ekans' eyes got wider. "Ooh, we're going to meet a ghost!"

"A wandering spirit," Machop corrected him dryly.

* * *

"Why in Kanto did you agree with her plans, Kammy?!" Gravelerette wailed. "I don't want to meet a ghost or a wandering spirit or a lost soul, whatever you call it! I don't want to!"

"We have no other choice," Kammy told her. "The medium said that this ghost won't let anyone get onto the top floor, and she said that there's an item up there. Maybe it's even a Hidden Machine. We can't afford to skip items. We need to get the ghost to go away."

"I wasn't hoping you would say that," moaned Gravelerette.

As we went higher up, a weird fog began to appear, getting thicker with every floor. Soon we couldn't even see the mediums scattered around the tombstones, so people were frequently coming out of the fog unexpectedly to have a battle.

"Oh, just our luck that we forgot to bring Pidgeotto along," sighed Ekans. "He could have used Defog to clear this horrible fog."

"Cheer up!" Diglett sang. "We may not be able to see people through this fog, but at least we can still see our hands in front of our faces!"

"Diglett, you don't have any hands," I reminded him. "Oh, right. I knew that," he sang.

Finally, I lost count of how many floors we had climbed up.

"This has got to be the floor below the top floor," Gravelerette wheezed. "This just has to."

"And if it isn't?" Machop teased. Gravelerette glared at her. "Don't even start."

"Looks like this is it," Kammy said to Gravelerette's relief. "There are fewer tombstones and people."

"Well, what are we waiting for, then?" Machop cried out excitedly. "Let's meet this lost soul!"

"Wait!" I cried, but I was too late. Machop had already bounded over to the stairs leading to the top floor.

And the next second, there was a wisp of strange purplish smoke, and then a pair of eyes, and then a mouth with rows and rows of gleaming sharp teeth!

"AAAAAAHHH!" Machop screeched, scrambling back in surprise and alarm.

"It's the ghost!" wailed Gravelerette.

"What can we do?" gasped Diglett.

"I don't know!" Kammy groaned. "I don't even know what kind of Pokémon that is!"

Suddenly I had a great idea. "Kammy, the machine!" I cried. "The Silph machine! The one that can see invisible things and stuff and such." The machine had been given to Kammy by the director of Silph Co. as a reward for having driven the Rockets out.

"Oh! Right! Good idea, Venusaur." She rummaged in her bag and pulled out a tiny machine shaped like a remote control with a single button on it. She pressed the button, and the wispy smoke drifted away to reveal the identity of the Pokémon.

Which looked spookily similar to Cubone.

Although it looked similar to Cubone, there were still a few differences. The skull on the ghost's head had practically merged with its head so that there were no peepholes at all, but its eyes had become one with the skull. Also, its bone club looked sturdier.

"Come on, Gravelerette! Battle time!" shouted Kammy, sending Gravelerette out.

"What?! Me?!" Gravelerette squeaked fearfully, but she had no choice but to face the ghost. However, the ghost was much faster than Gravelerette. It lunged forward with something that would have been a well-aimed Bonemerang.

Well, it would have hit, too, if it wasn't for Cubone, who suddenly appeared from behind a tombstone.

The ghost stopped abruptly mid-action. "My... son!" it rasped.


	5. Impostor

**The Great Pokemon Conspiracies:**

**~Missingno.~**

**...**

**Chapter Five: Impostor**

Everyone's mouths dropped open as Cubone crept forward. "Mother?" he whispered. "I... Is that really you? You look... Different."

"Yes, my son," the ghost said. "I'm now nothing but a wandering spirit" - or a lost soul, as Machop would have called it - "but I was your mother before the Rockets caught me. And being a spirit has, I'm afraid, altered my appearance. I may look different, Machop, but inside I'm your loving mother."

Cubone didn't know what to say, and neither did Kammy nor any of her Pokémon. Gravelerette's mouth was the widest open.

"Come here, my son," the ghost said. "Let me take a look at you one last time..."

Cubone edged forward.

"Come a little closer."

Cubone edged forward some more.

"Come on, dear, don't be afraid of your mother."

Cubone edged forward...

"STOP!"

Suddenly there was a thundering voice which set all of us on edge and stopped Cubone from nearing the ghost any more.

And the next second, another wisp of purple smoke appeared!

Another use of the Silph machine revealed the second ghost to be that of a kangaroo-like Pokémon with an empty pouch on its stomach.

"Stop all this nonsense at once!" it bellowed. Even Kammy, the Pokémon Trainer, obeyed.

The first ghost first looked surprised but then glared at the second ghost. "What's the meaning of this?!" she snapped. "Why are you keeping me away from my son?!"

But the second ghost paid her no attention. Instead she turned to Cubone. "Don't listen to her, my dear," she said gently. "You're not her son, not in the slightest. You're mine."


	6. Dear Ghost

**The Great Pokemon Conspiracies:**

**~Missingno.~**

**...**

**Chapter Six: Dear Ghost**

"Huh?! How can that be? Cubone's got two mothers?!" Gravelerette burst out.

"Of course he hasn't," Ekans snapped. "One of them must be a fake."

"And she's it!" shrieked the skull-headed ghost. "I'm Cubone's real mother! That impostor may look like your real mother, Cubone, but she's only trying to trick you! I'm your real mother!"

No, I am," the kangaroo one said calmly. "She's the fake one." She stretched a hand in Cubone's direction. "My son, my little son. I remember the games of leapfrog we used to play, and how you would hide in my pouch whenever you get scared. Oh, and of course I can't forget your favorite meal of Oran Berries - but you'll only eat the perfectly round ones."

Cubone gasped. It hit him like a brick. A mother is someone who knows you inside out, someone who perfectly knows your childhood although even certain events you've forgotten.

He turned cautiously to the skull-headed ghost. "Who are you?" he whispered.

"Gaaaahhh!" the skull-headed ghost bellowed in rage, found out. Suddenly, instead of disappearing, it turned into a weird shapeless creature - it was just a random mass of squiggles.

"Aaahhhh!" shrieked a frightened Gravelerette. She used Rock Blast to hit the weird creature, who hissed with rage at every hit. Then, Kammy's Trainer instinct led her hand into her bag and she grabbed a Poké Ball. She threw it at the creature, trapping it in. The next second, there was no other sound but the click of Kammy's Poké Ball.

"Oh, Cubone," said the remaining ghost. "My son, Cubone."

This time Cubone crept forward until he was close enough so the ghost could pat his head with an invisible hand.

"My son, you mustn't be too sad," she said. "You have to move on."

"I... I'll never forget you," Cubone wept.

"And neither will I," his mother smiled. "Now go, Cubone. Go and have adventures like you said you would when you were smaller. Don't be too lonely - I'll always be with you."

"Yes, mother," Cubone sniffed. "And I... I'll get re-revenge from the R-rockets!" His voice was a bit wobbly. "Won't I make them P-P-PAY!"

His mother smiled. "Goodbye, Cubone," she said. "G-g-goodbye," Cubone whispered, and the next second, she was gone.

"Wow," Kammy and the party were still staring wide-eyed at the thin air which Cubone's real mother had disappeared into.

Meanwhile, an overwhelmed Cubone ran like a frightened rabbit down the stairs, and the next moment, it was nothing but silence.


	7. Carry On Wayward Son

**The Great Pokemon Conspiracies:**

**~Missingno.~**

**...**

**Chapter Seven: Carry On Wayward Son**

Kammy found a tearful Cubone still weeping near the Lost Tower's entrance.

Kammy had found a soft spot for Cubone after what had just happened to him. She thought Cubone must have been through a lot.

"Hey," she said gently as she bent down.

Cubone did nothing but continue to weep.

"It must be tough to lose your mother," Kammy said. "Really tough indeed."

Cubone's skull rattled. "Really tough."

"But I heard what your mother said," Kammy said softly. "You've always wanted to go on adventures."

"I have," Cubone admitted, sniffling.

"Tell you what," Kammy said. "You can join our team if you want to. We'll have all sorts of adventures together."

The rest of the Pokémon and I looked at one another. Diglett was smiling. I think everyone thought this was a good idea, indeed.

"Yes, we'll go traveling to distant towns and have exciting battles," Machop exclaimed. "And I'll take you under my wing like a little brother," I added.

"You don't have any wings," Diglett giggled. "Just joking," he said when I gave him a look.

Cubone looked up at us. "And we'll beat the Rockets?" He sounded hopeful.

Kammy smiled. "Yes. We'll beat the Rockets."

Suddenly Cubone's eyes looked as if they'd gotten shinier.

"I'm in," he said.


	8. Epilogue

**The Great Pokemon Conspiracies:**

**~Missingno.~**

**...**

**EPILOGUE**

_Pallet Town, Kanto_

"I got a mail from Kammy!" Professor Oak exclaimed. "I wonder how she's getting on. Oh, and this time the letter comes with a package."

"I bet she's doing a great job," said the professor's aide. "But I wonder what's inside the package?"

Professor Oak opened Kammy's letter and read it. "Oh my," he said. "Very interesting. Very interesting indeed."

"What does Kammy say?"

"She believes she has found a new species of Pokémon!" exclaimed Oak. "In the Lost Tower, Lavender Town. And I suppose the Pokémon inside this Poké Ball is it."

His aide turned to see that he had ripped open the package to reveal a Poké Ball. "What? Isn't that a usual Marowak? The evolution of Cubone?"

But as they watched on, the Pokémon began to flicker back and forth between the skull-headed form and the shapeless form.

"Oh. It's a new species indeed," gasped the aide.

"I wonder if this Pokémon evolves into another Pokémon," Oak mused. "If it does, it may be another new species!"

A while later, Oak had arranged with his grandson and Kammy's friend Gary to train the mystery Pokémon. "I want you to see if it evolves or not," he told his grandson.

So Gary trained and trained it, and a few days later, he got the answer. The mystery Pokémon did evolve...

Into the same species of Pokémon Cubone's real mother was!

"Well, what do you know," Oak said once Gary had let him know the surprising result. "We never would have thought we'd be able to prove that our old theory is correct."

"What old theory?" Gary demanded.

"Well, we thought Cubone and Kangaskhan were related, but we couldn't find anything to prove it. Cubone look so similar to Kangaskhan babies, but the only difference is that Cubone wear skulls on their heads. We thought that there was something more than meets the eye here."

Gary tried to imagine a vision of a Cubone and a Kangaskhan baby in his head. He had to admit that they did look similar.

"This mysterious Pokémon is the missing link!" the aide exclaimed excitedly. "This is the missing link between Cubone's evolutionary line and the motherly Pokémon Kangaskhan! This is a new species so we must give it a name!"

"How about M, short for Missingno.?" Gary joked lightly.

"That's a great idea, Gary!" Oak's response startled him. "We'll call it Missingno.!"

THE END


End file.
